An NMR Perspective on Enzyme Dynamics

Structural proteomics of macromolecular assemblies using oxidative footprinting and mass spectrometry

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Entropy, Binding Energy, and Enzymic Catalysis

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Slow Internal Dynamics in Proteins: Application of NMR Relaxation Dispersion Spectroscopy to Methyl Groups in a Cavity Mutant of T4 Lysozyme

Mulder, F. A. A., Hon, B., Mittermaier, A., Dahlquist, F. W., & Kay, L. E. (2002) · Journal of the American Chemical Society · doi:10.1021/ja0119806 · Cited by 116

Can a pairwise contact potential stabilize native protein folds against decoys obtained by threading?

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Structural bases of hydrogen tunneling in enzymes: progress and puzzles

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Point mutations and sequence variability in proteins: Redistributions of preexisting populations

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Production of large quantities of isotopically labeled protein in Pichia pastoris by fermentation

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Evidence for Environmentally Coupled Hydrogen Tunneling during Dihydrofolate Reductase Catalysis

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Quantitative NMR Studies of High Molecular Weight Proteins: Application to Domain Orientation and Ligand Binding in the 723 Residue Enzyme Malate Synthase G

Tugarinov, V., & Kay, L. E. (2003) · Journal of Molecular Biology · doi:10.1016/s0022-2836(03)00238-9 · Cited by 105

Conformation Coupled Enzyme Catalysis: Single-Molecule and Transient Kinetics Investigation of Dihydrofolate Reductase

Antikainen, N. M., Smiley, R. D., Benkovic, S. J., & Hammes, G. G. (2005) · Biochemistry · doi:10.1021/bi051378i · Cited by 104

Contact Model for the Prediction of NMR N−H Order Parameters in Globular Proteins

Zhang, F., & Brüschweiler, R. (2002) · Journal of the American Chemical Society · doi:10.1021/ja027847a · Cited by 101

Comparison of Methyl Rotation Axis Order Parameters Derived from Model-Free Analyses of 2 H and 13 C Longitudinal and Transverse Relaxation Rates Measured in the Same Protein Sample

Ishima, R., Petkova, A. T., Louis, J. M., & Torchia, D. A. (2001) · Journal of the American Chemical Society · doi:10.1021/ja0104711 · Cited by 100

NMR Characterization of the Metallo-β-lactamase from Bacteroides fragilis and Its Interaction with a Tight-Binding Inhibitor: Role of an Active-Site Loop

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Conformational States of Bovine Pancreatic Ribonuclease A Observed by Normal and Partially Relaxed Carbon 13 Nuclear Magnetic Resonance

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Off-resonance rf fields in heteronuclear NMR: Application to the study of slow motions

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Enzyme Dynamics During Catalysis Measured by NMR Spectroscopy

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Conformational change in substrate binding, catalysis and product release: an open and shut case?

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Active Site Dynamics in the Lead-Dependent Ribozyme

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Double- and Zero-Quantum NMR Relaxation Dispersion Experiments Sampling Millisecond Time Scale Dynamics in Proteins

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Conformational dynamics and enzyme activity

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Complexity and simplicity of ligand–macromolecule interactions: the energy landscape perspective

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Ligand Binding Energy and Catalytic Efficiency from Improved Packing within Receptors and Enzymes

Williams, D. H., Stephens, E., & Zhou, M. (2003) · Journal of Molecular Biology · doi:10.1016/s0022-2836(03)00428-5 · Cited by 91

The 'dynamics' in the thermodynamics of binding.

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Nuclear magnetic resonance studies of sperm whale myoglobin specifically enriched with 13C in the methionine methyl groups.

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Allosteric Inhibition of Aminoglycoside Phosphotransferase by a Designed Ankyrin Repeat Protein

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Measurement of carbon-13 longitudinal relaxation using 1H detection

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Analysis of deuterium relaxation-derived methyl axis order parameters and correlation with local structure

Mittermaier, A., Kay, L. E., & Forman-Kay, J. D. (1999) · Journal of Biomolecular NMR · doi:10.1023/a:1008387715167 · Cited by 88

Flexibility and Ligand Exchange in a Buried Cavity Mutant of T4 Lysozyme Studied by Multinuclear NMR

Mulder, F. A. A., Hon, B., Muhandiram, D. R., Dahlquist, F. W., & Kay, L. E. (2000) · Biochemistry · doi:10.1021/bi001351t · Cited by 88

Protein Dynamics and Enzymatic Catalysis: Investigating the Peptidyl−Prolyl Cis−Trans Isomerization Activity of Cyclophilin A

Agarwal, P. K., Geist, A., & Gorin, A. A. (2004) · Biochemistry · doi:10.1021/bi0495228 · Cited by 88

15N NMR Relaxation Studies of Free and Inhibitor-Bound 4-Oxalocrotonate Tautomerase: Backbone Dynamics and Entropy Changes of an Enzyme upon Inhibitor Binding

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Delineation of the allosteric mechanism of a cytidylyltransferase exhibiting negative cooperativity.

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Promoting Vibrations in Human Purine Nucleoside Phosphorylase. A Molecular Dynamics and Hybrid Quantum Mechanical/Molecular Mechanical Study

Núñez, S., Antoniou, D., Schramm, V. L., & Schwartz, S. D. (2004) · Journal of the American Chemical Society · doi:10.1021/ja0457563 · Cited by 85

Theoretical study of R1ρ rotating-frame and R2 free-precession relaxation in the presence of n-site chemical exchange

Trott, O., & Palmer, A. G. I. (2004) · Journal of Magnetic Resonance · doi:10.1016/j.jmr.2004.06.005 · Cited by 83

Biosynthetic 13C Labeling of Aromatic Side Chains in Proteins for NMR Relaxation Measurements

Teilum, K., Brath, U., Lundström, P., & Akke, M. (2006) · Journal of the American Chemical Society · doi:10.1021/ja055660o · Cited by 82

Transverse 13 C Relaxation of CHD 2 Methyl Isotopmers To Detect Slow Conformational Changes of Protein Side Chains

Ishima, R., Louis, J. M., & Torchia, D. A. (1999) · Journal of the American Chemical Society · doi:10.1021/ja992836b · Cited by 82

Multiple Time Scale Backbone Dynamics of Homologous Thermophilic and Mesophilic Ribonuclease HI Enzymes

Butterwick, J. A., Loria, J. P., Astrof, N. S., Kroenke, C. D., Cole, R., Rance, M., & Palmer, A. G. I. (2004) · Journal of Molecular Biology · doi:10.1016/j.jmb.2004.03.055 · Cited by 81

Relationships between protein structure and dynamics from a database of NMR-derived backbone order parameters

Goodman, J. L., Pagel, M. D., & Stone, M. J. (2000) · Journal of Molecular Biology · doi:10.1006/jmbi.1999.3419 · Cited by 81

NMR Spectroscopy Tools for Structure‐Aided Drug Design

Homans, S. W. (2003) · Angewandte Chemie International Edition · doi:10.1002/anie.200300581 · Cited by 81

Effect of Cofactor Binding and Loop Conformation on Side Chain Methyl Dynamics in Dihydrofolate Reductase

Schnell, J. R., Dyson, H. J., & Wright, P. E. (2003) · Biochemistry · doi:10.1021/bi035464z · Cited by 78

NMR solution structure of the lead-dependent ribozyme: evidence for dynamics in RNA catalysis 1 1Edited by I. Tinoco

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Cyclophilin A complexed with a fragment of HIV-1 gag protein: insights into HIV-1 infectious activity

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Quantitative 13C and 2H NMR Relaxation Studies of the 723-Residue Enzyme Malate Synthase G Reveal a Dynamic Binding Interface

Tugarinov, V., & Kay, L. E. (2005) · Biochemistry · doi:10.1021/bi0519809 · Cited by 74

Structure of the Escherichia coli malate synthase G:pyruvate:acetyl‐coenzyme A abortive ternary complex at 1.95 Å resolution

Anstrom, D. M., Kallio, K., & Remington, S. J. (2003) · Protein Science · doi:10.1110/ps.03174303 · Cited by 74

Backbone dynamics and refined solution structure of the N-terminal domain of DNA polymerase β. Correlation with DNA binding and dRP lyase activity 1 1Edited by P. E. Wright

Maciejewski, M. W., Liu, D., Prasad, R., Wilson, S. H., & Mullen, G. P. (2000) · Journal of Molecular Biology · doi:10.1006/jmbi.1999.3455 · Cited by 74

Spectroscopic, Calorimetric, and Kinetic Demonstration of Conformational Adaptation in Peptide-Antibody Recognition

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Single-molecule and transient kinetics investigation of the interaction of dihydrofolate reductase with NADPH and dihydrofolate

Zhang, Z., Rajagopalan, P. T. R., Selzer, T., et al. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0400091101 · Cited by 72

Molecular Motions and Protein Folding: Characterization of the Backbone Dynamics and Folding Equilibrium of α2D Using13C NMR Spin Relaxation

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Conformational Substates Modulate Hydride Transfer in Dihydrofolate Reductase

Thorpe, I. F., & Brooks, C. L. (2005) · Journal of the American Chemical Society · doi:10.1021/ja053558l · Cited by 70

Isomorphous Crystal Structures of Escherichia coli Dihydrofolate Reductase Complexed with Folate, 5-Deazafolate, and 5,10-Dideazatetrahydrofolate: Mechanistic Implications

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Dynamic properties of proteins from NMR spectroscopy

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Preorganization and protein dynamics in enzyme catalysis

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Reaction path and free energy calculations of the transition between alternate conformations of HIV-1 protease

Rick, S. W., Erickson, J. W., & Burt, S. K. (1998) · Proteins Structure Function and Bioinformatics · Cited by 66

Domain Flexibility in Ligand-Free and Inhibitor-BoundEscherichia coliAdenylate Kinase Based on a Mode-Coupling Analysis of15N Spin Relaxation

Shapiro, Y. E., Kahana, E., Tugarinov, V., et al. (2002) · Biochemistry · doi:10.1021/bi012132q · Cited by 65

Conformational Change of H+-ATPase β Monomer Revealed on Segmental Isotope Labeling NMR Spectroscopy

Yagi, H., Tsujimoto, T., Yamazaki, T., Yoshida, M., & Akutsu, H. (2004) · Journal of the American Chemical Society · doi:10.1021/ja045279o · Cited by 65

Mechanistic Implication of Crystal Structures of the Cyclophilin−Dipeptide Complexes,

Zhao, Y., & Ke, H. (1996) · Biochemistry · doi:10.1021/bi960278x · Cited by 65

Comparison of 13CH3, 13CH2D, and 13CHD2 methyl labeling strategies in proteins

Ollerenshaw, J. E., Tugarinov, V., Skrynnikov, N. R., & Kay, L. E. (2005) · Journal of Biomolecular NMR · doi:10.1007/s10858-005-2614-2 · Cited by 64

Approaches to the Design of Effective HIV-1 Protease Inhibitors

Lebon, F., & Ledecq, M. (2000) · Current Medicinal Chemistry · doi:10.2174/0929867003375146 · Cited by 62

Functional conformational motions in the turnover cycle of cholesterol oxidase

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Strength of an Interloop Hydrogen Bond Determines the Kinetic Pathway in Catalysis byEscherichia coliDihydrofolate Reductase

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Hydrogen atoms in proteins: Positions and dynamics

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Transition structures for hydride transfers

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Improved labeling strategy for 13C relaxation measurements of methyl groups in proteins

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Deletion of a Highly Motional Residue Affects Formation of the Michaelis Complex for Escherichia coli Dihydrofolate Reductase

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NMR Relaxation Order Parameter Analysis of the Dynamics of Protein Side Chains

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Solution NMR methods for quantitative identification of chemical exchange in 15N‐labeled proteins

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Backbone Dynamics of trp Repressor Studied by 15N NMR Relaxation

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Estimation of Dynamic Parameters from NMR Relaxation Data using the Lipari–Szabo Model-Free Approach and Bayesian Statistical Methods

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Backbone Dynamics of Escherichia coli Adenylate Kinase at the Extreme Stages of the Catalytic Cycle Studied by 15N NMR Relaxation

Shapiro, Y. E., Sinev, M. A., Sineva, E. V., Tugarinov, V., & Meirovitch, E. (2000) · Biochemistry · doi:10.1021/bi992076h · Cited by 53

Backbone dynamics of Escherichia coli thioesterase/protease I: evidence of a flexible active-site environment for a serine protease 1 1Edited by M. F. Summers

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Substrate binding and enzyme function investigated by infrared spectroscopy

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Intramolecular Dynamics of Low Molecular Weight Protein Tyrosine Phosphatase in Monomer–Dimer Equilibrium Studied by NMR: A Model for Changes in Dynamics upon Target Binding

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In‐Cell NMR Spectroscopy

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Interloop Contacts Modulate Ligand Cycling during Catalysis byEscherichia coliDihydrofolate Reductase

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Prediction of methyl-side Chain Dynamics in Proteins

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Characterizing semilocal motions in proteins by NMR relaxation studies

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Characterization of two hydrophobic methyl clusters in HIV-1 protease by NMR spin relaxation in solution11Edited by P. E. Wright

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Flexibility and Function in HIV Protease: Dynamics of the HIV-1 Protease Bound to the Asymmetric Inhibitor Kynostatin 272 (KNI-272)

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Probing the Binding Entropy of Ligand–Protein Interactions by NMR

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Anisotropic rotational diffusion in model-free analysis for a ternary DHFR complex

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Structural and thermodynamic analysis of the binding of solvent at internal sites in T4 lysozyme

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Multiple States of the Tyr318Leu Mutant of Dihydroorotate Dehydrogenase Revealed by Single-Molecule Kinetics

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Consequences of Binding an S-Adenosylmethionine Analogue on the Structure and Dynamics of the Thiopurine Methyltransferase Protein Backbone

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The function of amino acid residues contacting the nicotinamide ring of NADPH in dihydrofolate reductase from Escherichia coli

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Correlation between 2H NMR Side-Chain Order Parameters and Sequence Conservation in Globular Proteins

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Investigation of Ligand Binding and Protein Dynamics in Bacillus subtilis Chorismate Mutase by Transverse Relaxation Optimized Spectroscopy−Nuclear Magnetic Resonance,

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Structural and Dynamic Studies on Ligand-Free Adenylate Kinase from Mycobacterium tuberculosis Revealed a Closed Conformation that Can Be Related to the Reduced Catalytic Activity,

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Phosphorylation and Flexibility of Cyclic-AMP-Dependent Protein Kinase (PKA) Using 31P NMR Spectroscopy

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Lateral Hopping Requires Molecular Rocking

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Relationship between Enzyme Specificity and the Backbone Dynamics of Free and Inhibited α-Lytic Protease,

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Ligand Binding Energy and Enzyme Efficiency from Reductions in Protein Dynamics

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13C NMR Relaxation Studies of Backbone and Side Chain Motion of the Catalytic Tyrosine Residue in Free and Steroid-Bound Δ5-3-Ketosteroid Isomerase

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A Monoclonal Antibody Induces Opening of a Coiled Coil

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Dynamic personalities of proteins

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The role of dynamic conformational ensembles in biomolecular recognition

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An introduction to NMR-based approaches for measuring protein dynamics

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Coupling of receptor conformation and ligand orientation determine graded activity

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Catalytic Contributions from Remote Regions of Enzyme Structure

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